No, typically one only leaves a single hook. For streamers, it is usually the rear hook. For nymphs, in my case, it is going to be the front hook. I'm sure some leave both hooks, but I do not, nor do most tier I know, especially steelhead fishers.
With regards to the OP's question, I typically go for a vertical loop if I'm using a rigid linkage such as mono or wire, but I also often use PowerPro or Fireline and in that case I do not leave a loop. Instead, I loop the line over the shank of the trailing hook three times and then pull the knot tight, creating sort of a snell knot (I'm sure it has a formal name, I just don't know what it is) to make sure that the hook stays in place. Like Buddy, I'm not sure it matters, but it is what I prefer for the reasons Uncle Jesse states.